This post is intended to act as a brief Situation Report (SITREP) about the genomic sequencing of the B.1.1.7 lineage of SARS-CoV-2 in USA.
As of 2021-01-14, there's been 14627 sequences detected in over 38 countries under this strain (see table for definition). In the US, there's been 73 sequences detected in over 8 states.
This report shows the prevalence at the state, national, and global level.
The table on the left contains the key mutations that represent the strain. The plot on the
right shows the genetic distance of B.1.1.7 genomes and the immediate outgroup of this lineage over time. This is also referred to as the root to tip plot.
| Gene | Nucleotide Mutations | Amino Acid Changes |
|---|---|---|
| ORF1ab | C3266T, T6953C, C5387A, 11288:11296 deletion | T1001I, I2230T, A1708D |
| S | A23062T, C23270A, A23402G, C23603A, C23708T, T24505G, G24913C | DEL69-70, DEL144Y, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H |
| N | GAT28279CTA, C28976T | D3L, S235F |
| ORF8 | G28047T, C27971T, A28110G | R52I, Q27_, Y73C |
As figure 3.2 indicates, the B.1.1.7 genomes in the US (so far),
were not a result of unbiased sequencing but were identified by S-gene
target failures (SGTF) in community-based diagnostic PCR testing. Since
it was not an unbiased approach, it does not indicate the true prevalence
of the B117 lineage in the US. This only tells us that the lineage is
present in the US.
P.S: estimates of true prevalence in the US are discussed in
this post